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<div  id='write'  class = 'is-mac'><h1><a name='header-c5' class='md-header-anchor '></a>三代转录组测序应用</h1><div class='md-toc' mdtype='toc'><p class="md-toc-content"><span class="md-toc-item md-toc-h1" data-ref="c5"><a class="md-toc-inner" href="#header-c5">三代转录组测序应用</a></span><span class="md-toc-item md-toc-h2" data-ref="c11"><a class="md-toc-inner" href="#header-c11">人类相关研究中的RNA测序</a></span><span class="md-toc-item md-toc-h2" data-ref="c41"><a class="md-toc-inner" href="#header-c41">动植物研究中的RNA测序</a></span><span class="md-toc-item md-toc-h2" data-ref="c74"><a class="md-toc-inner" href="#header-c74">鉴定细菌操纵子全长</a></span></p></div><p>在真核生物中，大多数基因都可以通过选择性剪接产生多种转录本，大大提高了基因组的蛋白质编码潜力[1]。来自相同基因的可变剪接产生的不同转录本可能具有显著差异，甚至拮抗作用[2]。短读长的RNA-seq不能跨越转录物的全长，难以整体表征转录本异构体的多样性[3]。</p><p>同种型测序（Iso-Seq）可以直接检测转录本的全长，消除了使用算法对转录本进行重建的步骤。Iso-Seq方法产生有关可变剪接的外显子和转录起始位点的准确信息。它还提供关于多聚腺苷酸化位点的信息，用于在目标基因或整个转录组中的全长异构体的长度达10 kb的转录物。</p><h2><a name='header-c11' class='md-header-anchor '></a>人类相关研究中的RNA测序</h2><p>因为大多数人类基因可选择剪接[1]，所以知道哪个同种型在样品中表达是准确研究和分析的关键。单个基因可能编码惊人数量的蛋白质，且在某些情况下具有相反的生物学功能[4]。剪接突变已经与各种疾病表型相关联，许多人类疾病与可变剪接异构体水平的变化有关（<a href='http://www.eurasnet.info/scientists/alternative-splicing-and-disease/list-of-diseases'>List of Diseases</a>）。从短读长数据进行转录本重建缺乏敏感性和特异性，这使得RNA测序数据的解释复杂化[5]。</p><p><strong>Iso-seq在人转录组研究中的亮点：</strong></p><ul><li>直接进行全长转录本测序，无需重建转录本；</li><li>对转录多样性进行广泛或有针对性的研究，以获得关于替代转录的频率和类型的关键信息；</li><li>特异性地观察等位基因的表达；</li><li>区分细胞、组织和疾病状态之间的同种型表达。</li></ul><p><strong>特色研究：</strong>在良好表征的细胞系中发现新的同种型[6]</p><p><img src='https://ws2.sinaimg.cn/large/006tKfTcgy1fhp9ty2yi9j30o2075404.jpg' alt='1' /></p><p>科学家在人类胚胎干细胞系中共发现了2,428种新型异构体，其中216种新型基因表现出差异表达。该研究同时证明三代Iso-seq能够提高二代RNA-seq数据的定量准确度。</p><p><strong>特色研究：</strong>鉴定前列腺癌（Castration-Resistant Prostate Cancer，CRPR）中的新型同种型</p><p><img src='https://ws2.sinaimg.cn/large/006tKfTcgy1fhp9u6bb4uj30i90yntem.jpg' alt='2' /></p><p>科学家们使用长读序列来鉴定和量化在CRPC中表达的全长雄激素受体（AR）同种型。他们确定了截短的同种型AR-V9，其显示出比AR-靶向治疗的主要抗性AR-V7更具预测性的生物标志物。<a href='http://www.pacb.com/wp-content/uploads/Clark_AACR_2017_SMRT-sequencing-of-full-length-androgen-receptor-isoforms-in-prostate-cancer.pdf'>了解更多</a></p><h2><a name='header-c41' class='md-header-anchor '></a>动植物研究中的RNA测序</h2><p>单个基因可编码的蛋白质数量有时多得让人惊讶，每个蛋白质又具有不同的生物学功能，在高等生物中更是如此。短读长测序因为打断了转录本，所以在组装时会产生错误或不完全捕获，丢失一些我们想要的信息。</p><p>利用单分子实时测序可以得到无需组装的全长转录本，能够进行如下研究：</p><ul><li>做直接的，循证基因的注释；</li><li>在已经有充分研究的转录组中发现新的基因和同种型；</li><li>在综合基因模型中鉴定启动子和剪接位点以了解基因调控；</li><li>提高用于基因表达研究的同种型水平分辨率的RNA-seq定量的准确性；</li><li>区分重要的应激反应，发育和组织特异性同种型。</li></ul><p><strong>特色研究：</strong>发现鸡中数以千计的新型异构体[7]</p><p><img src='https://ws4.sinaimg.cn/large/006tKfTcgy1fhp9ufla2sj30o208ggly.jpg' alt='3' /></p><p>Gladstone研究所的科学家们使用PacBio Iso-Seq数据来改善鸡基因组的注释。他们确定了超过9,000种新的转录同种型，包括替代转录起始位点、心脏特异性同种型和反义转录事件的这些实例。</p><p><strong>特色研究：</strong>显著提高高粱基因组注释[8]</p><p><img src='https://ws3.sinaimg.cn/large/006tKfTcgy1fhp9ulqv6oj30jy0crmym.jpg' alt='4' /></p><p>该文使用Iso-Seq方法在高粱转录组中的剪接异构体分析大大改善了基因组注释，确定了超过77,000个新型剪接异构体和超过2,100个新基因。在这个例子中，发现一个基因产生73个新的可变剪接的同种型，而先前的基因模型只含有一个单一的同种型。</p><h2><a name='header-c74' class='md-header-anchor '></a>鉴定细菌操纵子全长</h2><p><strong>特色研究：</strong>原核转录组和宏转录组的全长cDNA测序</p><p><img src='https://ws2.sinaimg.cn/large/006tKfTcgy1fhp9urucw1j30o20armym.jpg' alt='5' /></p><p>细菌全长转录组测序具有将细菌操纵子转录可视化和检测操纵子与备选起点和停止位点全长转录本的能力。使用SMRT®测序可轻松获得多顺反子和全长操纵子序列，无需组装短片段。<a href='http://www.pacb.com/wp-content/uploads/Full_length_cDNA_Sequencing_of_Prokaryotic_Transcriptome_and_Metatranscriptome_Samples.pdf'>了解更多</a></p><hr /><p><strong>参考文献</strong></p><p>[1]	Q. Pan, O. Shai, L. J. Lee, et al., Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing[J]. Nat Genet. 2008, 40(12):1413-1415.</p><p>[2]	L. H. Boise, M. González-García, C. E. Postema, et al., bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death[J]. Cell. 1993, 74(4):597-608.</p><p>[3]	T. Steijger, J. F. Abril, P. G. Engstrom, et al., Assessment of transcript reconstruction methods for RNA-seq[J]. Nat Meth. 2013, 10(12):1177-1184.</p><p>[4]	C. Schwerk and K. Schulze-Osthoff, Regulation of apoptosis by alternative pre-mRNA splicing[J]. Mol Cell. 2005, 19(1):1-13.</p><p>[5]	I. Korf, Genomics: the state of the art in RNA-seq analysis[J]. Nat Meth. 2013, 10(12):1165-1166.</p><p>[6]	K. F. Au, V. Sebastiano, P. T. Afshar, et al., Characterization of the human ESC transcriptome by hybrid sequencing[J]. Proceedings of the National Academy of Sciences. 2013, 110(50):E4821-E4830.</p><p>[7]	S. Thomas, J. G. Underwood, E. Tseng, et al., Long-Read Sequencing of Chicken Transcripts and Identification of New Transcript Isoforms[J]. PloS ONE. 2014, 9(4):e94650.</p><p>[8]	S. E. Abdel-Ghany, M. Hamilton, J. L. Jacobi, et al., A survey of the sorghum transcriptome using single-molecule long reads[J]. Nature Communications. 2016, 7:11706.</p></div>
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